Effects of rehydration on physiological and transcriptional responses of a water-stressed rhizobium

다국어 초록 (Multilingual Abstract)

As a microsymbiont of soybean, Bradyrhizobium japonicum plays an important role in symbiotic nitrogen fixation and sustainable agriculture. However, the survival of B. japonicum cells under water-deplete (e.g., drought) and water-replete (e.g., flood) conditions is a major concern affecting their nitrogen-fixing ability by establishing the symbiotic relationship with the host. In this study, we isolated a water stress tolerant rhizobium from soybean root nodules and tested its survival under water-deplete conditions. The rhizobium was identified as Bradyrhizobium japonicum and named strain 5038. Interestingly, both plate counting and live/dead fluorescence staining assays indicate that a number of viable but non-culturable cells exist in the culture medium upon the rehydration process which could cause dilution stress. Bradyrhizobium japonicum 5038 cells increased production of exopolysaccharide (EPS) and trehalose when dehydrated, suggesting that protective responses were stimulated. As expected, cells reduced their production upon the subsequent rehydration.
To examine differential gene expression of B. japonicum 5038 when exposed to water-deplete and subsequent waterreplete conditions, whole-genome transcriptional analysis was performed under 10% relative humidity (RH), and subsequent 100% RH, respectively. A total of 462 differentially expressed genes (DEGs, > 2.0-fold) were identified under the 10% RH condition, while 3,776 genes showed differential expression during the subsequent rehydration (100% RH) process. Genes involved in signal transduction, inorganic ion transport, energy production and metabolisms of carbohydrates, amino acids, and lipids were far more up-regulated than downregulated in the 10% RH condition. Notably, trehalose biosynthetic genes (otsAB, treS, and treYZ), genes ligD, oprB, and a sigma factor rpoH were significantly induced by 10% RH.
Under the subsequent 100% RH condition, genes involved in transcription, translation, cell membrane regulation, replication and repair, and protein processing were highly up-regulated.
Interestingly, most of 10%-RH inducible genes displayed rehydration-repressed, except three genes encoding heat shock (Hsp20) proteins. Therefore, this study provides molecular evidence for the switch of gene expression of B. japonicum cells when encountered the opposite water availability from water-deplete to water-replete conditions.

참고문헌 (Reference)

1 Tian, T., "agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update" 45 : W122-W129, 2017

2 Lebre, P. H., "Xerotolerant bacteria : surviving through a dry spell" 15 : 285-296, 2017

3 Bernard, T., "Variations in the response of salt-stressed Rhizobium strains to betaines" 143 : 359-364, 1986

4 Basler, M., "Type VI secretion dynamics within and between bacterial cells" 337 : 815-, 2012

5 Heinrich, J., "Two proteolytic modules are involved in regulated intramembrane proteolysis of Bacillus subtilis RsiW" 74 : 1412-1426, 2009

6 McIntyre, H. J., "Trehalose biosynthesis in Rhizobium leguminosarum bv. trifolii and its role in desiccation tolerance" 73 : 3984-3992, 2007

7 Chen, Y., "Transcriptome response to drought, rehydration and re-dehydration in potato" 21 : 159-, 2020

8 Domínguez, F. A., "Transcriptome profiling reveals the importance of plasmid pSymB for osmoadaptation of Sinorhizobium meliloti" 188 : 7617-7625, 2006

9 LaVoie, S. P., "Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure" 19 : 52-, 2018

10 Singh, J., "Transcriptional response of Saccharomyces cerevisiae to desiccation and rehydration" 71 : 8752-8763, 2005

11 Cytryn, E. J., "Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress" 189 : 6751-6762, 2007

12 Basler, M., "Tit-for-Tat: Type VI secretion system counterattack during bacterial cell-cell Interactions" 152 : 884-894, 2013

13 Busch, A. W., "The tryptophan-rich sensory protein (TSPO) is involved in stress-related and light-dependent processes in the cyanobacterium Fremyella diplosiphon" 6 : 1393-, 2015

14 Alves, B. J. R., "The success of BNF in soybean in Brazil" 252 : 1-9, 2003

15 Schnider-Keel, U., "The sigma factor AlgU(AlgT)controls exopolysaccharide production and tolerance towards desiccation and osmotic stress in the biocontrol agent Pseudomonas fluorescens CHA0" 67 : 5683-5693, 2001

16 Oliver, M. J., "The rehydration transcriptome of the desiccation–tolerant bryophyte Tortula ruralis : transcript classification and analysis" 5 : 89-, 2004

17 Setlow, P., "The germination of spores of Bacillus species : what we know and don’t know" 196 : 1297-1305, 2014

18 Battesti, A., "The RpoS-mediated general stress response in Escherichia coli" 65 : 189-213, 2011

19 Gourion, B., "The PhyR-σEcfG signalling cascade is involved in stress response and symbiotic efficiency in Bradyrhizobium japonicum" 73 : 291-305, 2009

20 Graham, P.H., "Stress tolerance in Rhizobium and Bradyrhizobium, and nodulation under adverse soil conditions" 38 : 475-484, 1992

21 Kosanke, J. W., "Slow rehydration improves the recovery of dried bacterial populations" 38 : 520-525, 1992

22 Salema, M. P., "Rupture of nodule bacteria on drying and rehydration" 14 : 15-22, 1982

23 Reina-Bueno, M., "Role of trehalose in heat and desiccation tolerance in the soil bacterium Rhizobium etli" 12 : 207-, 2012

24 Heeb, S., "Role of the stress sigma factor RpoS in GacA/RsmA-controlled secondary metabolism and resistance to oxidative stress in Pseudomonas fluorescens CHA0" 243 : 251-258, 2005

25 Zahran, H. H., "Rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in an arid climate" 63 : 968-989, 1999

26 Vriezen, J. A. C., "Responses of rhizobia to desiccation in relation to osmotic stress, oxygen, and temperature" 73 : 3451-3459, 2007

27 Humann, J. L., "Regulatory and DNA repair genes contribute to the desiccation resistance of Sinorhizobium meliloti Rm1021" 75 : 446-453, 2009

28 López-Leal, G., "RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock" 15 : 770-, 2014

29 Read, R. R., "Purification and characterization of adhesive exopolysaccharides from Pseudomonas putida and Pseudomonas fluorescens" 33 : 1080-1090, 1987

30 Lehman, A. P., "OxyR-Dependent transcription response of Sinorhizobium meliloti to oxidative stress" 200 : e00622–17-, 2018

31 Boncompagni, E., "Occurrence of choline and glycine betaine uptake and metabolism in the family Rhizobiaceae and their roles in osmoprotection" 65 : 2072-2077, 1999

32 Oono, Y., "Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca. 7000 full-length cDNA microarray" 34 : 868-887, 2003

33 Gayoso, C. M., "Molecular mechanisms involved in the response to desiccation stress and persistence in Acinetobacter baumannii" 13 : 460-476, 2014

34 Lennon, J. T., "Microbial seed banks : the ecological and evolutionary implications of dormancy" 9 : 119-130, 2011

35 O’Callaghan, M., "Microbial inoculation of seed for improved crop performance : issues and opportunities" 100 : 5729-5746, 2016

36 Scherber, C. M., "Membrane phase behavior of Escherichia coli during desiccation, rehydration, and growth recovery" 1788 : 2427-2435, 2009

37 Deaker, R., "Legume seed inoculation technology : a review" 36 : 1275-1288, 2004

38 Kanehisa, M., "KEGG: new perspectives on genomes, pathways, diseases and drugs" 45 : D353-D361, 2017

39 Kocharunchitt, C., "Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157 : H7 Sakai to steady-state conditions of cold and water activity stress" 11 : M111.00901-, 2012

40 Tapia, H., "Increasing intracellular trehalose is sufficient to confer desiccation tolerance to Saccharomyces cerevisiae" 112 : 6122-6127, 2015

41 Riedel, K., "Identification of proteins involved in osmotic stress response in Enterobacter sakazakii by proteomics" 7 : 1217-1231, 2007

42 Vanderlinde, E. M., "Identification of a novel ABC transporter required for desiccation tolerance, and biofilm formation in Rhizobium leguminosarum bv. viciae 3841" 71 : 327-340, 2010

43 Busse, M. D., "Growth and nodulation responses of Rhizobium meliloti to water stress induced by permeating and nonpermeating solutes" 55 : 2431-2436, 1989

44 Gruzdev, N., "Global transcriptional analysis of dehydrated Salmonella enterica serovar Typhimurium" 78 : 7866-7875, 2012

45 LeBlanc, J. C., "Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1" 74 : 2627-2636, 2008

46 Kocharunchitt, C., "Global genome response of Escherichia coli O157 : H7 Sakai during dynamic changes in growth kinetics induced by abrupt downshift in water activity" 9 : e90422-, 2014

47 Donati, A. J., "Genome-wide transcriptional and physiological responses of Bradyrhizobium japonicum to paraquat-mediated oxidative stress" 77 : 3633-3643, 2011

48 Katoh, H., "Gene expression in the cyanobacterium Anabaena sp. PCC7120 under desiccation" 47 : 164-174, 2004

49 Sugawara, M., "Functional role of Bradyrhizobium japonicum trehalose biosynthesis and metabolism genes during physiological stress and nodulation" 76 : 1071-1081, 2010

50 Streeter, J. G., "Factors affecting the survival of Bradyrhizobium applied in liquid cultures to soya bean [Glycine max (L.) Merr.] seeds" 103 : 1282-1290, 2007

51 Galperin, M. Y., "Expanded microbial genome coverage and improved protein family annotation in the COG database" 43 : D261-D269, 2015

52 Robinson, A., "Essential biological processes of an emerging pathogen: DNA replication, transcription, and cell division in Acinetobacter spp" 74 : 273-297, 2010

53 Ahn, S. J., "Effects of oxygen on virulence traits of Streptococcus mutans" 189 : 8519-8527, 2007

54 Kim, K. Y., "Effect of nutrients on biofilm formation by Listeria monocytogenes on stainless steel" 58 : 24-28, 1995

55 Trapnell, C., "Differential analysis of gene regulation at transcript resolution with RNA-seq" 31 : 46-53, 2012

56 Osa-Afiana, L. O., "Differences among cowpea rhizobia in tolerance to high temperature and desiccation in soil" 43 : 435-439, 1982

57 Mary, P., "Differences among Rhizobium meliloti and Bradyrhizobium japonicum strains in tolerance to desiccation and storage at different relative humidities" 26 : 1125-1132, 1994

58 Deaker, R., "Desiccation tolerance of rhizobia when protected by synthetic polymers" 39 : 573-580, 2007

59 Vriezen, J. A. C., "Desiccation responses and survival of Sinorhizobium meliloti USDA 1021 in relation to growth phase, temperature, chloride and sulfate availability" 42 : 172-178, 2006

60 Hansen, L. T., "Desiccation of adhering and biofilm Listeria monocytogenes on stainless steel : survival and transfer to salmon products" 146 : 88-93, 2011

61 Vriezen, J. A. C., "Desiccation induces viable but non-culturable cells in Sinorhizobium meliloti 1021" 2 : 6-, 2012

62 Bae, N., "Deciphering the functions of the outer membrane porin OprBXo involved in virulence, motility, exopolysaccharide production, biofilm formation and stress tolerance in Xanthomonas oryzae pv. oryzae" 19 : 2527-2542, 2018

63 Vincent, J. M., "Death of root nodule bacteria on drying" 13 : 258-270, 1962

64 Salema, M. P., "Death of rhizobia on inoculated seed" 14 : 13-14, 1982

65 Dupuy, P., "DNA double-strand break repair is involved in desiccation resistance of Sinorhizobium meliloti, but is not essential for its symbiotic interaction with Medicago truncatula" 163 : 333-342, 2017

66 Jiang, W., "CspA the major cold-shock protein of Escherichia coli" 272 : 196-202, 1997

67 Tamaru, Y., "Crucial role of extracellular polysaccharides in desiccation and freezing tolerance in the terrestrial cyanobacterium Nostoc commune" 71 : 7327-7333, 2005

68 Galkiewicz, J. P., "Cross-kingdom amplification using Bacteria-specific primers : complications for studies of coral microbial ecology" 74 : 7828-7831, 2008

69 Zhang, Q., "Correlation of intracellular trehalose concentration with desiccation resistance of soil Escherichia coli populations" 78 : 7407-7413, 2012

70 Zeidler, S., "Coping with low water activities and osmotic stress in Acinetobacter baumannii: significance, current status and perspectives" 21 : 2212-2230, 2019

71 Toh, H., "Complete genome sequence of Lactobacillus acetotolerans RIB 9124(NBRC 13120)isolated from putrefed(hiochi)Japanese sake" 214 : 214-215, 2015

72 Jeon, J. M., "Characterization of a functional role of the Bradyrhizobium japonicum isocitrate lyase in desiccation tolerance" 16 : 16695-16709, 2015

73 Van de Mortel, M., "Cell envelope components contributing to biofilm growth and survival of Pseudomonas putida in low-water-content habitats" 52 : 735-750, 2004

74 Sleator, R. D., "Bacterial osmoadaptation : the role of osmolytes in bacterial stress and virulence" 26 : 49-71, 2002

75 Hengge-Aronis, R., "Back to log phase : σS as a global regulator in the osmotic control of gene expression in Escherichia coli" 21 : 887-893, 1996

76 Atieno, M., "Aqueous peat extract exposes rhizobia to sublethal stress which may prime cells for improved desiccation tolerance" 102 : 7521-7539, 2018

77 Chang, W. S., "Alginate production by Pseudomonas putida creates a hydrated microenvironment and contributes to biofilm architecture and stress tolerance under water-limiting conditions" 189 : 8290-8299, 2007

78 Aranda, J., "Acinetobacter baumannii RecA protein in repair of DNA damage, antimicrobial resistance, general stress response, and virulence" 193 : 3740-3747, 2011

79 Davey, M. E., "A homologue of the tryptophan-rich sensory protein TspO and FixL regulate a novel nutrient deprivation-induced Sinorhizobium meliloti locus" 66 : 5353-5359, 2000