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Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis.

1. Introduction

Riemerella anatipestifer (R. anatipestifer, RA) is a Gram-negative bacterium that belongs to the family Flavobacteriaceae in the rRNA superfamily V [1]. R. anatipestifer infection causes disease in ducks, geese, chickens, turkeys, and other waterfowl and birds [2]. The disease presents as an acute or chronic septicemia characterized by meningitis, fibrinous pericarditis, perihepatitis, and other symptoms [3]. The disease causes increased mortality and decreased weight and is estimated to result in huge economic losses to the duck industry each year worldwide. At present, at least 21 serotypes of R. anatipestifer have been identified in the world [2, 4].

Iron is one of the most important elements for bacterial growth, as it is an essential cofactor in many important enzymes involved in energy metabolism and nucleotide synthesis [5]. Iron is the second most abundant metal on earth, but it exists primarily in the insoluble ferric oxide form under aerobic conditions, which is not available for bacterial growth [5]. Inside the host, most iron is bound to iron-binding proteins, such as ferritin, transferrin, and lactoferrin. Iron could also be included in the heme of hemoproteins (the terminology "heme" was used when talking about hemoproteins) [6]. Bacteria employ various mechanisms to capture iron from the outside [7]. One of these mechanisms is the secretion of a small molecular compound, a siderophore, which sequesters iron from the outside environment by high-affinity interactions [8]. Then, iron-bound siderophores are taken up by the bacteria through specific siderophore receptors and transport systems [9]. Alternatively, some pathogens have specific cell surface receptors that bind hemin (the terminology "hemin" was used when talking about iron and protoporphyrin ring source) or hemoprotein and transport hemin to the cell or secreted hemophores that capture hemin from host hemoproteins and then deliver hemin to bacterial surface receptors [10]. Therefore, iron-limited conditions are able to prompt most bacteria to upregulate the expression of genes related to iron/hemin uptake, such as iron/hemin transporters and siderophore biosynthetic enzymes [11-13].

R. anatipestifer requires iron and hemin to survive [14]. Genome analysis has shown that R. anatipestifer codes for a large number of TonB-dependent receptors, a TonB family protein, two sets of TonB complexes, and an FeoAB system [15]. In a previous study, we demonstrated that TonB1 and TonB2 are involved in hemin uptake by R. anatipestifer ATCC11845 [14]. Moreover some hemin binding proteins were detected in R. anatipestifer CH-1 [16]. However, other genes involved in iron/hemin uptake by R. anatipestifer are largely unknown. In this study, we analyzed the global transcriptomic changes in R. anatipestifer CH-1 under iron-limited conditions. Here, we observed wide-ranging effects on the transcripts of iron-related genes of R. anatipestifer CH-1 and identified some new genes involved in iron/hemin uptake.

2. Materials and Methods

2.1. Bacterial Strains and Growth Conditions. For transcriptome analyses, R. anatipestifer CH-1 was grown in tryptone soy broth (TSB) medium (Sigma, China) as the iron-replete condition, while the iron-limited condition was TSB supplemented with 100 [micro]M iron chelator 2,2'-dipyridyl (Dip). The bacteria were cultured at 37[degrees]C with shaking at 180 rpm/min. Then, they were harvested at OD600 = 0.6 for iron-limited cultures and OD600 = 1.1 for iron-replete cultures (Figure 1).

2.2. RNA-Seq. Total RNA extraction was performed using the RNeasy Protect Bacteria Mini Kit (QIAGEN, Cat. number 74524) using the protocol described by Liu et al. [17]. A total amount of 3 [micro]g RNA per sample was used for the RNA sample preparations. RNA quantification, library preparation, and sequencing were performed at Beijing Novogene as described elsewhere. Then the clean data were obtained by removing reads containing adapter, reads containing ployN, and low-quality reads from raw data [18]. The high-quality reads obtained for each library were shown in Table 1. Then the R. anatipestifer CH-1 genome (CP003787.1) and gene model annotation files were downloaded from genome website ( directly, using Bowtie2-2.2.3 to build index and align clean reads of the R. anatipestifer CH-1 genome [19].

2.3. Real-Time PCR Validation of RNA-Seq. The differential expression of selected genes was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using the SYBR green-based detection system on a CFX Connect[R] Real-Time PCR Detection System (BioRad Laboratories, Hercules, CA) using the KAPA SYBR[R] FAST qPCR kit (KAPABIOSYSTEMS, Boston, USA). cDNA was synthesized from each RNA sample (1 [micro]g) using the HiScript[TM] Q RT SuperMix for qPCR (+gDNA wiper) (R123-01; Vazyme, Nanjing, China). Real-time PCR assays were conducted with the primers for real-time PCR listed in Table S1 in Supplementary Material, available online at Quantitative PCR was performed on samples deposited in triplicate using the standard curve mode protocol in which the calibration curve was generated using serial fivefold dilutions of 100 ng of total RNA. The RNA quantity was normalized using a probe specific for 16S rRNA.

2.4. RNA-Seq Analysis. To quantify the expression level of genes, HTSeq v0.6.1 was used to count the read numbers mapped to each gene [20]. Then, the FPKM (expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) of each gene was calculated based on the length of the gene and the read counts mapped to this gene. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor [21]. In this study, we used the DEGSeq R package (1.20.0) to execute the differential expression analysis of two conditions [22]. Corrected P value of 0.005 and log2 (fold change) of 1 were set as the threshold for significantly differential expression. To analyze the gene structure of R. anatipestifer CH-1, Rockhopper was used to identify operons and transcription start sites. This program can be used for efficient and accurate analysis of bacterial RNA-Seq data and can aid in the elucidation of bacterial transcriptomes [23]. Moreover we used the aligned paired-end reads to infer the operonic structure of R. anatipestifer CH-1 transcripts. If genes obtained >20 reads aligning on both genes in a sequencing sample, they would be selected as potential in an operonic structure. Sequential genes that are present in operonic structure were merged together to form potential operonic transcripts (Table S2).

3. Results and Discussion

3.1. Growth ofR. anatipestifer CH-1 in TSB and TSB with Dip. To evaluate the effect of iron restriction on the growth of R. anatipestifer CH-1, we grew R. anatipestifer CH-1 in TSB and TSB with 100 [micro]M Dip, which restricts most iron. Figure 1 showed that the growth of R. anatipestifer CH-1 was seriously hindered when iron was restricted, indicating that iron is an essential element for R. anatipestifer. Thus, this condition was suitable for performing RNA-Seq.

3.2. General Assessment of Iron Limitation Transcriptomic Datasets. Over 95% of all clean reads aligned to coding regions of the R. anatipestifer CH-1 genome (Table 1). Since only one sample in the different iron condition was used to perform RNA-Seq, qRT-PCR validation was performed on the transcriptome data using a subset of 20 differentially regulated genes (Table S1). The transcriptome data generally corresponded well with the qRT-PCR data, with a Pearson correlation coefficient of 0.806 (Figure 2), illustrating that our RNA-Seq data were of suitable quality for transcriptome analysis.

Upon comparing cultures grown in TSB and TSB with Dip, overall differences in gene expression were observed (Figure 3). To examine these differences further, DEGs (differentially expressed genes) were identified using the DEseq package [22]. A total of 463 DEGs were identified, including 80 upregulated (Table 2) and 383 downregulated genes (Table S3). These genes represent 23% of the genome (2038 genes) [15]. The large number of DEGs suggests that iron-limited environments have global effects on R. anatipestifer CH-1. Since samples of different OD were used to perform RNASeq, this study can not exclude the fact that cell density might influence gene expression.

3.3. Genome-Wide Identification of R. anatipestifer CH-1 Genes in Operonic Structures. In addition to identifying gene boundaries, we drew on paired-end sequencing information to identify the R. anatipestifer CH-1 global operonic structure. In total, 377 genes were determined to be in operonic structures using this analysis, thus constituting 230 operons (Table S2). These genes represent 18% of the genome (2038 genes) [15].

3.4. Gene Ontology (GO) Annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Mapping of DEGs. The DEGs were assigned to 26 functional groups by enrichment analysis of Gene Ontology (GO) assignments [18]. In the three main GO categories of biological process, cellular component, and molecular function, genes in the role categories of "localization, transport, and establishment of localization" in biological process, "membrane" in cellular component or "receptor activity and transporter activity" in molecular function were notably up- or downregulated (Figure 4).

The biological functions associated with the DEGs were further analyzed in terms of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways [24], and a total of 20 pathways were predicted (Figure 5). Among these pathways, "microbial metabolism in diverse environments," "ribosome," and "thiamine metabolism" were the most highly represented categories (Figure 5).

3.5. Iron Limitation Increased the Transcription of Putative Iron Acquisition Systems. Genome sequence analysis indicated that R. anatipestifer CH-1 encodes [Fe.sup.2+] and [Fe.sup.3+] acquisition systems [15]. Once in the periplasm, [Fe.sup.2+] is taken across the inner membrane via a divalent metal uptake system, such as the Feo system of E. coli [25] and the Yfe system of Yersinia pestis [26]. In this study, the predicted genesfeoB (B739_0594) andfeoA (B739_0595), which encode an [Fe.sup.2+] transporter, were highly upregulated in the iron-limited condition, suggesting a role in the uptake of ferrous iron (Table 2). Sequence comparison revealed that all of the sequenced R. anatipestifer genomes have homologues of FeoA and FeoB of R. anatipestifer CH-1, with similarities of 100% for FeoA and between 88% and 100% for FeoB. In turn, these R. anatipestifer CH-1 genes have 33.45% and 32.89% identities to the FeoA and FeoB products of E. coli, respectively. In E. coli, this operon is regulated by Fur and is induced in acidic conditions [27]. The functions of FeoA and FeoB and their regulation in R. anatipestifer are underinvestigated.

In aerobic conditions, many bacteria produce siderophores to solubilize [Fe.sup.3+]. Then, siderophore-bound [Fe.sup.3+] is taken up by TonB-dependent receptors [5]. Genome analysis revealed that there are at least 33 predicted TonB-dependent receptors in R. anatipestifer CH-1, some of which are predicted transporters for ferric-siderophore complexes or heme. In this study, 5 TonB-dependent receptors were upregulated (B739_0094, B739_0103, B739_0173, B739_1068, and B739_1416) in the presence of iron depletion. The expression levels of seven other putative TonB-dependent transporters (B739_0115, B739_0876, B739_1045, B739_1343, B739_0216, B739_0329, and B739_0389) (Table S3) were downregulated in the presence of iron depletion. Upregulated TonB-dependent receptors would be predicted to be involved in iron or hemin uptake, while the functions of all downregulated TonB-dependent receptors are presently unknown. Similar results have been obtained in other bacteria, such as Pseudomonas fluorescens [28].

TonB-dependent receptors rely on the accessory proteins ExbB, ExbD, and TonB for energy transduction. One TonB family protein and two sets of ExbB-ExbD-TonB were found and identified in R. anatipestifer [14]. In other bacteria, such as E. coli [29] and Pseudomonas fluorescens [28], the tonB gene is negatively regulated by iron. However, the transcription of tonB genes in R. anatipestifer CH-1 was not significantly changed in the iron-limited condition. To ensure the validity of the result, we also used qRT-PCR to measure tonB gene transcription in iron-limited conditions. The result was coincident with that of RNA-Seq. These results suggested that, in contrast to many bacteria, the tonB systems of R. anatipestifer CH-1 are not regulated by iron.

Once siderophore-bound [Fe.sup.3+] is transported into the cytoplasm, the iron must be released from the siderophore. The first mechanism is that siderophore-bound Fe(III) is reduced to siderophore-bound Fe(II) followed by its spontaneous release due to the low affinity of iron Fe(II) with the siderophore. Another mechanism is that siderophore-bound Fe(III) is hydrolyzed by specialized enzymes, leading to a dramatic loss of complex stability and facilitating the subsequent removal of the iron [30] in a reduction process. In this study, a gene coding for a siderophore-interacting protein (B739_0608) was upregulated significantly in the presence of iron depletion. This siderophore-interacting protein is involved in iron acquisition and virulence in R. anatipestifer strain CH-3 [31]. Surprisingly, among the upregulated genes, we did not find any homologue gene related to siderophore synthesis.

3.6. A Putative Polysaccharide Utilization Locus ofR. anatipestifer CH-1 Was Upregulated in Iron-Limited Conditions. In Capnocytophaga canimorsus, a member of the Bacteroidetes, a polysaccharide utilization system uses serotransferrin as an iron source [32]. Each polypeptide encoded by this locus is required for this iron uptake activity [32]. This type of system was named the iron capture system (ICS), and it contains seven genes: icsA, icsC, icsD, icsE, icsF, icsG, and icsH [32]. In this study, we identified a gene cluster (B739_0094, B739_0095, B739_0096, B739_0097, B739_0098, B739_0099, B739_0100, B739_0101, B739_0102, and B739_0103) (Table 2) involved in polysaccharide utilization, the expression of which was upregulated in the presence of iron depletion. Sequence comparison showed that the homologues of icsC, icsD, icsE, icsF, icsG, and icsH from Capnocytophaga canimorsus are B739_0103, B739_0102, B739_0101, B739_0100, B739_0099, and B739_0098, respectively, in the R. anatipestifer CH-1 genome. The homologue of icsA, B739_1068, was not cotranscribed with the others. Interestingly, some genes that were upregulated in the gene cluster, such as B739_0094, B739_0095, B739_0096, and B739_0097, were not predicted to contribute to the ICS system. Additionally, the R. anatipestifer CH-1 genome contains at least 6 polysaccharide utilization systems. In iron-limited conditions, three of the genes (locus B739_0094-B739_0103, locus B739_2091-B739_2093, and locus B739_0310-B739_0312) were upregulated (Table 2), while three other genes (locus B739_0115-B739_0118, locus B739_0875-B739_0876, and locus B739_1044-B739_1045) were downregulated (Table S3). Why some loci were upregulated and some loci were downregulated in the iron-limited condition is not currently understood.

3.7. Iron Limitation Increased Transcription of Putative Hemin Acquisition Systems. In the host, heme-containing proteins, such as hemoglobin, can be used as the main iron source by pathogenic bacteria [33]. Hemin uptake systems are regulated by iron in other bacteria [34, 35]. Here, putative genes involved in hemin uptake were more highly expressed in iron-limited cultures of R. anatipestifer CH-1 than in iron-replete cultures. Within the upregulated genes, the most highly expressed gene cluster was FepA-hmuY (B739_1416, B739_1417), which encodes a putative outer membrane ferrienterochelin, a colicin receptor and an HmuY-like hemophore protein. In Porphyromonas gingivalis, HmuY is a heme-binding lipoprotein associated with the outer membrane or secreted to the outside environment [36, 37]. Gene (B739_1415) adjacent to the FepA-hmuY operon was also upregulated in iron-limited medium. The functions of B739_1415, B739_1416, and B739_1417 in hemin utilization are underinvestigated in our group.

3.8. Transcription of Respiratory Chain Genes. In aerobic metabolism, the respiratory chain typically uses proteins that require iron as a cofactor [38]. When R. anatipestifer CH-1 was grown in iron-limited medium, the expression of genes coding for cytochrome biogenesis protein (B739_0948), periplasmic cytochrome c552 subunit (B739_0946), and cytochrome C (B739_0186) were downregulated (Table S3). It indicated that iron restriction hindered R. anatipestifer aerobic metabolism. Similarly, in other bacteria, such as Pseudomonas fluorescens Pf-5, the transcription levels of genes encoding cytochrome c-type biogenesis proteins (PFL_1684-88) and subunits of cbb3-type cytochrome c oxidases (PFL_1922-25, PFL_2834) are downregulated in iron-limited versus iron-replete medium [28].

3.9. Transcription of Genes Related to Natural Competence. Natural transformation refers to the process by which bacteria can actively take up and integrate exogenous DNA. Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays a prominent role in bacterial evolution [39]. The process of Vibrio cholerae natural transformation involves four steps: DNA-binding via type IV pili, DNA pulling via ComEA, DNA translocation via ComEC, and DNA recombination by the single-strand DNA-binding proteins DprA and RecA [40]. Previously, we found that R. anatipestifer CH-1 is naturally competent [41]. In R. anatipestifer CH-1, no putative type IV pilus locus is evident in the genome. In R. anatipestifer CH-1, two proteins that are predicted to be involved in the DNA uptake process, a ComEC homologue (B739_1095) and a gene encoding a single-strand DNA-binding protein (B739_1757), were downregulated in iron-limited conditions. One possibility for this phenomenon is that these proteins require iron for activity, as well as iron being predicted to be involved in the natural transformation process. This relationship between natural transformation and iron availability has not yet been described.

4. Conclusion

In this study, we examined the transcriptomic impact of iron limitation on R. anatipestifer CH-1 by comparing iron-limited TSB cultures with iron-replete TSB cultures. This transcriptome analysis identified numerous genes involved in R. anatipestifer CH-1 iron utilization. Under iron limitation, we observed changes in the transcription levels of genes related to iron homeostasis functions, such as the Feo system, the ICS system, and other iron uptake systems. Iron limitation also resulted in several unexpected responses, particularly the increased transcription of the ribosomal protein genes L18, L15, and L31. The data in this study were useful for identifying genes involved in iron utilization in R. anatipestifer CH-1 and for shedding light on the adaptation mechanisms of R. anatipestifer CH-1 in iron-limited environments, such as hosts.

RNA-Seq:      RNA sequencing
qRT-PCR:      Quantitative reverse transcription
              polymerase chain reaction
HGT:          Horizontal gene transfer
DEGs:         Differentially expressed genes
KEGG:         Kyoto encyclopedia of genes and genomes
GO:           Gene Ontology
ICS:          Iron capture system
FPKM:         Expected number of Fragments Per
              Kilobase of transcript sequence per
              Million base pairs sequenced.

Conflicts of Interest

The authors declare that they have no competing interests.

Authors' Contributions

MaFeng Liu and AnChun Cheng conceived and designed the experiments. MaFeng Liu and Mi Huang performed the experiments. Francis Biville, MingShu Wang, DeKang Zhu, RenYong Jia, Shun Chen, and KunFeng Sun analyzed the data. Ying Wu and Qiao Yang contributed reagents/materials/analysis tools. MaFeng Liu and Mi Huang wrote the paper. All authors have reviewed the manuscript. MaFeng Liu and Mi Huang contributed equally to this work.


This work was supported by the International S&T Cooperation Program of Sichuan Province (Grant no. 2016HH0052), the National Natural Science Foundation of China (Grant no. 31302131,, the Research Fund for the Doctoral Program of Higher Education of China (Grant no. 20135103120006,, the National Science and Technology Support Program (no. 2015BAD12B05), the China Agricultural Research System (CARS-43-8), and the Integration and Demonstration of Key Technologies for Duck Industrialization in Sichuan Province (2014NZ0030).


[1] S. Subramaniam, K.-L. Chua, H.-M. Tan, H. Loh, P. Kuhnert, and J. Frey, "Phylogenetic position of Riemerella anatipestifer based on 16S rRNA gene sequences," International Journal of Systematic Bacteriology, vol. 47, no. 2, pp. 562-565, 1997.

[2] S. Subramaniam, B. Huang, H. Loh et al., "Characterization of a predominant immunogenic outer membrane protein of Riemerella anatipestifer," Clinical and Diagnostic Laboratory Immunology, vol. 7, no. 2, pp. 168-174, 2000.

[3] S. Leavitt and M. Ayroud, "Riemerella anatipestifer infection of domestic ducklings," Canadian Veterinary Journal, vol. 38, no. 2, p. 113, 1997.

[4] P. Pathanasophon, P. Phuektes, T. Tanticharoenyos, W. Narongsak, and T. Sawada, "A potential new serotype of Riemerella anatipestifer isolated from ducks in Thailand," Avian Pathology, vol. 31, no. 3, pp. 267-270, 2002.

[5] C. Wandersman and P. Delepelaire, "Bacterial iron sources: From siderophores to hemophores," Annual Review of Microbiology, vol. 58, pp. 611-647, 2004.

[6] L. J. Runyen-Janecky, "Role and regulation of heme iron acquisition in gram-negative pathogens," Frontiers in Cellular and Infection Microbiology, vol. 4, article 55, 2013.

[7] S. C. Andrews, A. K. Robinson, and F. Rodriguez-Quinones, "Bacterial iron homeostasis," FEMS Microbiology Reviews, vol. 27, no. 2-3, pp. 215-237, 2003.

[8] R. C. Hider and X. Kong, "Chemistry and biology of siderophores," Natural Product Reports, vol. 27, no. 5, pp. 637-657, 2010.

[9] N. Noinaj, M. Guillier, T. J. Barnard, and S. K. Buchanan, "TonB-dependent transporters: regulation, structure, and function," Annual Review of Microbiology, vol. 64, pp. 43-60, 2010.

[10] S. Cescau, H. Cwerman, S. Letoffe, P. Delepelaire, C. Wandersman, and F. Biville, "Heme acquisition by hemophores," BioMetals, vol. 20, no. 3-4, pp. 603-613, 2007.

[11] J. P. McHugh, F. Rodriguez-Quinones, H. Abdul-Tehrani et al., "Global iron-dependent gene regulation in Escherichia coli: a new mechanism for iron homeostasis," Journal of Biological Chemistry, vol. 278, no. 32, pp. 29478-29486, 2003.

[12] C. Yu, R. McClure, K. Nudela, N. Daou, and C. A. Genco, "Characterization of the Neisseria gonorrhoeae Iron and Fur regulatory network," Journal of Bacteriology, vol. 198, no. 16, pp. 2180-2191, 2016.

[13] J. Butcher and A. Stintzi, "The transcriptional landscape of Campylobacter jejuni under iron replete and iron limited growth conditions," PLoS ONE, vol. 8, no. 11, Article ID e79475, 2013.

[14] H. Liao, X. Cheng, D. Zhu et al., "TonB energy transduction systems of riemerella anatipestifer are required for iron and hemin utilization," PLoS ONE, vol. 10, no. 5, Article ID e0127506, 2015.

[15] X. Wang, W. Liu, D. Zhu et al., "Comparative genomics of Riemerella anatipestifer reveals genetic diversity," BMC Genomics, vol. 15, no. 1, article 479, 2014.

[16] H. Liao, M. Liu, X. Cheng et al., "The detection of hemin-binding proteins in riemerella anatipestifer CH-1," Current Microbiology, vol. 72, no. 2, pp. 152-158, 2016.

[17] M. Liu, M. Wang, D. Zhu et al., "Investigation of TbfA in Riemerella anatipestifer using plasmid-based methods for gene over-expression and knockdown," Scientific Reports, vol. 6, p. 37159, 2016.

[18] J. Liu, S. Wang, T. Qin et al., "Whole transcriptome analysis of Penicillium digitatum strains treatmented with prochloraz reveals their drug-resistant mechanisms," BMC Genomics, vol. 16, no. 1, article 855, 2015.

[19] B. Langmead and S. L. Salzberg, "Fast gapped-read alignment with Bowtie 2," Nature Methods, vol. 9, no. 4, pp. 357-359, 2012.

[20] S. Anders, P. T. Pyl, and W. Huber, "HTSeq--a Python framework to work with high-throughput sequencing data," Bioinformatics, vol. 31, no. 2, pp. 166-169, 2015.

[21] M. D. Robinson, D. J. McCarthy, and G. K. Smyth, "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data," Bioinformatics, vol. 26, no. 1, pp. 139-140, 2010.

[22] S. Anders and W. Huber, "Differential expression analysis for sequence count data," Genome Biology, vol. 11, no. 10, article R106, 2010.

[23] R. McClure, D. Balasubramanian, Y. Sun et al., "Computational analysis of bacterial RNA-Seq data," Nucleic Acids Research, vol. 41, no. 14, article e140, 2013.

[24] X. Mao, T. Cai, J. G. Olyarchuk, and L. Wei, "Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary," Bioinformatics, vol. 21, no. 19, pp. 3787-3793, 2005.

[25] C. K. Y. Lau, K. D. Krewulak, and H. J. Vogel, "Bacterial ferrous iron transport: the Feo system," FEMS Microbiology Reviews, vol. 40, no. 2, Article ID fuv049, pp. 273-298, 2016.

[26] S. W. Bearden and R. D. Perry, "The Yfe system of Yersinia pestis transports iron and manganese and is required for full virulence of plague," Molecular Microbiology, vol. 32, no. 2, pp. 403-414, 1999.

[27] J. Cao, M. R. Woodhall, J. Alvarez, M. L. Cartron, and S. C. Andrews, "EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH [Fe.sup.2+] transporter that is cryptic in Escherichia coli K-12 but functional in E. coli O157:H7," Molecular Microbiology, vol. 65, no. 4, pp. 857-875, 2007.

[28] C. K. Lim, K. A. Hassan, S. G. Tetu, J. E. Loper, and I. T. Paulsen, "The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5," PLoS ONE, vol. 7, no. 6, Article ID e39139, 2012.

[29] P. I. Higgs, R. A. Larsen, and K. Postle, "Quantification of known components of the Escherichia coli TonB energy transduction system: TonB, ExbB, ExbD and FepA," Molecular Microbiology, vol. 44, no. 1, pp. 271-281, 2002.

[30] M. Miethke and M. A. Marahiel, "Siderophore-based iron acquisition and pathogen control," Microbiology and Molecular Biology Reviews, vol. 71, no. 3, pp. 413-451, 2007.

[31] J. Tu, F. Lu, S. Miao et al., "The siderophore-interacting protein is involved in iron acquisition and virulence of riemerella anatipestifer strain CH3," Veterinary Microbiology, vol. 168, no. 2-4, pp. 395-402, 2014.

[32] P. Manfredi, F. Lauber, F. Renzi, K. Hack, E. Hess, and G. R. Cornelis, "New iron acquisition system in Bacteroidetes," Infection and Immunity, vol. 83, no. 1, pp. 300-310, 2015.

[33] T. A. Rouault, "Pathogenic bacteria prefer heme," Science, vol. 305, no. 5690, pp. 1577-1578, 2004.

[34] H. Contreras, N. Chim, A. Credali, and C. W. Goulding, "Heme uptake in bacterial pathogens," Current Opinion in Chemical Biology, vol. 19, no. 1, pp. 34-41, 2014.

[35] J. R. Sheldon and D. E. Heinrichs, "Recent developments in understanding the iron acquisition strategies of gram positive pathogens," FEMS Microbiology Reviews, vol. 39, no. 4, pp. 592-630, 2015.

[36] T. Olczak, A. Sroka, J. Potempa, and M. Olczak, "Porphyromonas gingivalis HmuY and HmuR: further characterization of a novel mechanism of heme utilization," Archives of Microbiology, vol. 189, no. 3, pp. 197-210, 2008.

[37] H. Wojtowicz, T. Guevara, C. Tallant et al., "Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis," PLoS Pathogens, vol. 5, no. 5, p. e1000419, 2009.

[38] U. A. Ochsner, P. J. Wilderman, A. I. Vasil, and M. L. Vasil, "GeneChip[R] expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes," Molecular Microbiology, vol. 45, no. 5, pp. 1277-1287, 2002.

[39] J. P. Gogarten and J. P. Townsend, "Horizontal gene transfer, genome innovation and evolution," Nature Reviews Microbiology, vol. 3, no. 9, pp. 679-687, 2005.

[40] N. Matthey and M. Blokesch, "The DNA-uptake process of Naturally Competent Vibrio cholerae," Trends in Microbiology, vol. 24, no. 2, pp. 98-110, 2016.

[41] M. Liu, L. Zhang, L. Huang et al., "Use of Natural Transformation To Establish an Easy Knockout Method in Riemerella anatipestifer," Applied and Environmental Microbiology, vol. 83, no. 9, 2017.

MaFeng Liu, (1, 2, 3) Mi Huang, (1, 2, 3) DeKang Zhu, (2, 3) MingShu Wang, (1, 2, 3) RenYong Jia, (1, 2, 3) Shun Chen, (1, 2, 3) KunFeng Sun, (1, 2, 3) Qiao Yang, (1, 2, 3) Ying Wu, (1, 2, 3) Francis Biville, (4) and AnChun Cheng (1, 2, 3)

(1) Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China

(2) Research Center of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan 611130, China

(3) Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China

(4) Unite des Infections Bacteriennes Invasives, Departement Infection et Epidemiologie, Institut Pasteur, Paris, France

Correspondence should be addressed to MaFeng Liu; and AnChun Cheng;

Received 28 December 2016; Accepted 29 March 2017; Published 30 April 2017

Academic Editor: Ernesto Picardi

Caption: Figure 1: Growth curves of R. anatipestifer CH-1 in iron-limited and iron-replete media. Optical densities at a wavelength of 600 nm were taken from the 2nd to the 18th hours at intervals of 2 hours. Measurements were performed on triplicate samples.

Caption: Figure 2: Validation of RNA-Seq data. Correlation analysis of [log.sub.2]-based fold changes between RNA-Seq data and qRT-PCR data for 20 genes of R. anatipestifer CH-1. The chart depicts a plot of RNA-Seq [log.sub.2]-based fold changes versus qRT-PCR [log.sub.2]- based fold changes for transcripts of genes in cultures of R. anatipestifer CH-1 grown in TSB+Dip medium versus TSB medium. A Pearson correlation coefficient of 0.806 was noted.

Caption: Figure 3: Differential gene transcription in cells grown in iron- limited TSB medium compared to TSB medium. The x-axis of the chart shows log2-based fold changes of transcripts in cells grown in iron-limited medium or TSB medium. The y-axis of the chart shows the statistical significance. Each dot in the chart represents one annotated gene. Red dots: upregulated, green dots: downregulated, and blue dots: no significant change.

Caption: Figure 4: Role categories of genes from the transcriptome data. The numbers of genes that are up- and downregulated in R. anatipestifer CH-1 grown in iron-limited TSB medium versus TSB medium are categorized according to role categories. Some genes are listed in more than one category and so may be counted more than once.

Caption: Figure 5: KEGG pathway enrichment analysis of differentially expressed genes between TSB and TSB with Dip. The y-axis of the chart shows the pathway name. The x-axis of the chart shows the Richness factor. The size of each point shows the number of genes in the pathway. The color of each point shows the Q value range.
Table 1: Summary of Illumina RNA-Seq data.

Sample       Total reads    Total mapped    Clean data *

CH_1TSB        17948156       17106745          2.24
CH_1TSBD       21489778       21099289          2.68

Sample        Percentage of
             sequence reads

CH_1TSB          95.31%
CH_1TSBD         98.18%

* Clean data were obtained from raw data by removing
reads containing adapter and poly-N and low-quality reads.

Table 2: Genes upregulated in Riemerella anatipestifer
CH-1 in iron-depleted conditions.

Gene ID      Gene name    log2.Fold_      P value

13715178     B739_0074       1.289       0.00021641

13715197     B739_0093      2.8509      2.72E - 108

13715198     B739_0094      1.2615       8.08E - 28

13715199     B739_0095      1.5902       5.31E - 23

13715200     B739_0096      3.3265      4.50E - 246

13715201     B739_0097      3.1172      1.67E - 115

13715202     B739_0098      3.3417           0

13715203     B739_0099      3.5712      5.25E - 128

13715204     B739_0100      3.5135      5.06E - 149

13715205     B739_0101      3.0646      1.23E - 132

13715206     B739_0102      3.4075           0

13715207     B739_0103      3.8099           0

13715231     B739_0127       1.275       1.56E - 06

13715277     B739_0173      3.3109      2.55E - 195

13715278     B739_0174      3.6434      5.92E - 216

13715279     B739_0175       2.413       5.96E - 53

13715280     B739_0176      3.0584       1.11E - 20

13715281     B739_0177      1.0467       3.85E - 06

13715373     B739_2137      1.1196       6.02E - 07

13715432     B739_0891      1.0093       1.05E - 06

13715452     B739_0912      1.0968       6.65E - 11

13715453     B739_0913      1.0147       0.0019348

13715513     B739_0973      1.0814       1.74E - 42

13715515     B739_0975      1.0712       4.92E - 15

13715522     B739_0982      1.1625       3.94E - 41

13715525     B739_0985      1.2524       1.07E - 63

13715526     B739_0986      1.0086      2.96E - 104

13715542        -//-        1.4285       1.38E - 29

13715606     B739_1068      3.8593           0

13715627     B739_1089      1.3526       1.76E - 65

13715649     B739_1112      1.0673       5.05E - 41

13715783     B739_1246      1.0718       1.24E - 91

13715836     B739_1299      1.2361       5.75E - 09

13715897     B739_1360      1.3576       0.0002407

13715932     B739_1395      1.4655       1.89E - 17

13715934     B739_1397       1.08        1.36E - 93

13715952     B739_1415      4.7103           0

13715953     B739_1416      3.7691           0

13715954     B739_1417      4.5479      5.15E - 244

13715956     B739_1419      1.2458       2.43E - 15

13716000     B739_1467       1.605       7.16E - 26

13716023     B739_1491      1.2534       2.55E - 67

13716028     B739_1496      1.0255       0.00022217

13716038     B739_1506      1.2051       1.41E - 13

13716056     B739_1525      1.0126       2.76E - 16

13716068     B739_1537      1.1923       2.42E - 35

13716179     B739_1648      1.1687       1.56E - 06

13716365     B739_1842      1.4584       1.63E - 10

13716406     B739_1883      1.1398       2.85E - 14

13716420     B739_1898      1.1221       8.61E - 20

13716438     B739_1916      1.1349       1.80E - 07

13716459     B739_1938      1.0469      7.76E - 115

13716524     B739_2003      1.1565       1.21E - 26

13716533     B739_2012      1.3031       0.0098864

13716610     B739_2089      1.0236       0.00048509

13716613     B739_2092      1.0406       3.79E - 32

13716712     B739_0221      1.0457       3.80E - 21

13716745     B739_0254      1.1712       1.78E - 48

13716748     B739_0257      1.0548       1.69E - 11

13716800     B739_0310      1.1729       4.55E - 21

13716803     B739_0313      1.0601       2.33E - 59

13716804     B739_0314      1.3277       1.60E - 56

13716824     B739_0335      1.2846       9.72E - 16

13716825     B739_0336      1.0435       1.66E - 07

13716826     B739_0337      1.0406       3.10E - 06

13716848     B739_0360      1.2725      1.12E - 137

13716849     B739_0361      1.0413       1.23E - 42

13716885     B739_0397      1.0567       6.51E - 19

13716908     B739_0420      1.0126       2.35E - 05

13716924     B739_0436       1.019       0.00033736

13716964     B739_0476      1.2682       6.15E - 21

13716978     B739_0490      2.3711       4.94E - 95

13717035     B739_0547      1.2256       9.53E - 39

13717082     B739_0594       1.082       1.16E - 21

13717083     B739_0595       2.259       5.94E - 27

13717096     B739_0608      1.6768       3.57E - 11

13717113     B739_0625      1.7097       2.66E - 21

13717239     B739_0753      1.1957       3.41E - 12

13717245     B739_0759      1.1112       2.64E - 14

Gene ID      Description

13715178     Hypothetical protein

13715197     Hypothetical protein

13715198     Outer membrane
             receptor for

13715199     Type I

13715200     Hypothetical protein

13715201     Carbohydrate-
             binding protein

13715202     Hypothetical protein

13715203     Hypothetical protein

13715204     Hypothetical protein

13715205     Substrate import-
             associated zinc

13715206     Glycan metabolism
             protein RagB

13715207     TonB/linked outer
             membrane protein,
             SusC/RagA family

13715231     DNA-binding protein

13715277     TonB-dependent
             receptor CirA,
             mostly Fe transport

13715278     Hypothetical protein

13715279     Ankyrin

13715280     Predicted
             periplasmic protein

13715281     Nitric oxide synthase

13715373     Camphor resistance
             protein CrcB;
             integral membrane
             protein possibly
             involved in
             condensation [cell
             division and

13715432     Hypothetical protein

13715452     Ribonuclease III

13715453     Hypothetical protein

13715513     50S ribosomal
             protein L16/L10E

13715515     30S ribosomal
             protein S17

13715522     50S ribosomal
             protein L18

13715525     50S ribosomal
             protein L15

13715526     Preprotein
             translocase subunit

13715542     tRNA-Glu

13715606     FecA

13715627     Hypothetical protein

13715649     50S ribosomal
             protein L31

13715783     30S ribosomal
             protein S16

13715836     Hypothetical protein

13715897     Hypothetical protein

13715932     2-Amino-4-hydroxy-

13715934     Outer membrane

13715952     Hypothetical protein

13715953     FepA

13715954     HmuY

13715956     Restriction
             endonuclease S
             subunits, Hsds

13716000     Hypothetical protein

13716023     Hypothetical protein

13716028     Hypothetical protein

13716038     Phosphate transport

13716056     OmpA

13716068     Thioredoxin

13716179     Hypothetical protein

13716365     Hypothetical protein

13716406     Preprotein
             translocase subunit

13716420     3-Oxoacyl-(acyl-
             synthase III

13716438     Hypothetical protein

13716459     Hypothetical protein

13716524     Polyisoprenoid-
             binding protein;
             YceI-like domain

13716533     Prevent-host-death
             protein; Antitoxin
             Phd_YefM, type II

13716610     Porin

13716613     Starch binding outer
             membrane protein

13716712     Gliding motility
             protein GldL

13716745     Hypothetical protein

13716748     Hypothetical protein

13716800     Carbohydrate-
             binding protein SusD

13716803     Ribonuclease G

13716804     Bacterial nucleoid
             DNA-binding protein

13716824     Hypothetical protein

13716825     Hypothetical protein

13716826     Ras_like_GTPase

13716848     50S ribosomal
             protein L11

13716849     Transcription

13716885     IMP dehydrogenase/
             GMP reductase

13716908     Sec-independent
             protein secretion
             pathway component

13716924     Predicted

13716964     Hypothetical protein

13716978     Ferritin-like domain

13717035     RNA polymerase Rpb6

13717082     Iron transporter FeoB

13717083     Iron transporter FeoA

13717096     Oxidoreductase;
             interacting protein
             [inorganic ion
             transport and

13717113     RNA polymerase sigma

13717239     Transthyretin-like

13717245     Iron-sulfur binding
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Title Annotation:Research Article
Author:Liu, MaFeng; Huang, Mi; Zhu, DeKang; Wang, MingShu; Jia, RenYong; Chen, Shun; Sun, KunFeng; Yang, Qi
Publication:BioMed Research International
Article Type:Report
Date:Jan 1, 2017
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