The Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean

Abstract

Sinorhizobium fredii HH103 is a fast-growing rhizobial strain infecting a broad range of legumes including both American and Asiatic soybeans. In this work, we present the sequencing and annotation of the HH103 genome (7.25 Mb), consisting of one chromosome and six plasmids and representing the structurally most complex sinorhizobial genome sequenced so far. Comparative genomic analyses of S. fredii HH103 with strains USDA257 and NGR234 showed that the core genome of these three strains contains 4,212 genes (61.7% of the HH103 genes). Synteny plot analysis revealed that the much larger chromosome of USDA257 (6.48 Mb) is colinear to the HH103 (4.3 Mb) and NGR324 chromosomes (3.9 Mb). An additional region of the USDA257 chromosome of about 2 Mb displays similarity to plasmid pSfHH103e. Remarkable differences exist between HH103 and NGR234 concerning nod genes, flavonoid effect on surface polysaccharide production, and quorum-sensing systems. Furthermore a number of protein secretion systems have been found. Two genes coding for putative type III-secreted effectors not previously described in S. fredii, nopI and gunA, have been located on the HH103 genome. These differences could be important to understand the different symbiotic behavior of S. fredii strains HH103, USDA257, and NGR234 with soybean.

The Sinorhizobium (Ensifer) fredii HH103 Nodulation Outer Protein NopI Is a Determinant for Efficient Nodulation of Soybean and Cowpea Plants

“…The analysis of the complete genome of HH103 (GenBank accession numbers HE616890 to HE616893, HE616899, CDSA010000001 to CDSA010000004, and LN735562) allowed the identification of several potential effectors that showed no homologies with other proteins from animal-or plant-pathogenic microorganisms, such as NopC, NopI, NopL, and NopP, and hence can be considered Rhizobium specific (34).…”

“…The nopI gene (858 bp), preceded by a conserved tts box, is located on plasmid c, which does not contain the T3SS gene cluster (34) (Fig. 1).…”

“…Four of them, nopC, nopI, nopL, and nopP, have only been described in rhizobia and, therefore, can be considered Rhizobium specific (18,34). In spite of the amino acid sequences of NopI and NopP sharing certain similarities ( Fig.…”

The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3

“…syrM, nodD3, and syrA appear to be universal in the Sinorhizobium genus based on published genome sequences (95)(96)(97)(98)(99)(100)(101)(102)(103)(104). Among S. meliloti and S. medicae strains, the orthologous proteins are nearly identical, and the gene arrangement is syntenic to S. meliloti Rm1021 (Fig.…”

Sinorhizobium fredii HH103 nolR and nodD2 mutants gain capacity for infection thread invasion of Lotus japonicus Gifu and Lotus burttii

“…The nodD1 and nodD2 sequences of S. fredii USDA191, USDA257, NGR234, CCBAU45436 and HH103 are very well conserved (Appelbaum et al, ; Krishnan et al, ; Schmeisser et al, ; Tian et al, ; Vinardell et al, ). However, the predicted USDA191 NodD2 protein is 55 amino acids shorter than those of the rest of S. fredii strains analysed so far (Fellay et al, ; Vinardell et al, ). The identity among the amino acid sequences of the proteins encoded by nodD1 and nodD2 is 69% in S. fredii USDA257 and USDA191 (Machado et al, ) and 62% in strain NGR234.…”