Identification and Comparative Genomic Analysis of Type VI Secretion Systems and Effectors in Klebsiella pneumoniae

Abstract

Klebsiella pneumoniae is a nosocomial opportunistic pathogen that can cause pneumonia, liver abscesses, and infections of the bloodstream. The resistance and pathogenicity of K. pneumoniae pose major challenges to clinical practice. However, the ecology and pathogenic mechanisms of K. pneumoniae have not been fully elucidated. Among these mechanisms, the secretion systems encoded by strains of the bacteria confer adaptive advantages depending on the niche occupied. The type VI secretion system (T6SS) is a multi-protein complex that delivers effector proteins to the extracellular environment or directly to eukaryotic or prokaryotic cells. T6SSs are widely distributed in Gram-negative bacteria and play an important role in bacterial virulence and the interactions between bacteria and other microorganisms or the environment. This study aimed to enhance the understanding of the characteristics of T6SSs in K. pneumoniae through an in-depth comparative genomic analysis of the T6SS in 241 sequenced strains of K. pneumoniae. We identified the T6SS loci, the synteny of the loci in different species, as well as the effectors and core T6SS-related genes in K. pneumoniae. The presence of a T6SS was a common occurrence in K. pneumoniae, and two T6SS clusters are the most prevalent. The variable region downstream of the gene vgrG usually encodes effector proteins. Conserved domain analysis indicated that the identified putative effectors in K. pneumoniae had the functions of lipase, ribonuclease, deoxyribonuclease, and polysaccharide hydrolase. However, some effectors did not contain predicted functional domains, and their specific functions have yet to be elucidated. This in silico study represents a detailed analysis of T6SS-associated genes in K. pneumoniae and provides a foundation for future studies on the mechanism(s) of T6SSs, especially effectors, which may generate new insights into pathogenicity and lead to the identification of proteins with novel antimicrobial properties.

Role of Klebsiella pneumoniae Type VI secretion system (T6SS) in long-term gastrointestinal colonization

“…In agreement with previously published data 28 , 29 , 33 , 36 , 40 , in silico analysis detected T6SS-related genes in both hypervirulent and non-hypervirulent K. pneumoniae strains and in other Klebsiella species irrespective of the strains’ virulence and their origin of isolation. The T6SS prevalence ranged from 98% in K. pneumoniae species to 14% in K. quasipneumoniae similpneumoniae , suggesting that a strong counter selection had occurred in this subspecies, which includes mostly lower virulent strains with less extensive antibiotic resistance 41 .…”

“…Although 80% of ST11 isolates of K. pneumoniae belong to this group, this is not the case for the ST2 isolate CH1157 strain. As previously mentioned, three tli1 encoding genes, which could serve as Tle1 immunity proteins, were found upstream tle1 in T6SS-1 cluster 36 . Tle1 phospholipase recruitment requires a DUF4123 adaptor to be fixed on the tip of the T6SS syringe before delivery.…”

“…In accordance with the classification proposed by Li et al, a DUF2235 domain is present in the protein sequence encoded by the tle1 gene, its specific function is not known. The presence of such a domain in CH1157 Tle1, allows its affiliation into the 4th effector group 36 . Although 80% of ST11 isolates of K. pneumoniae belong to this group, this is not the case for the ST2 isolate CH1157 strain.…”

“…1 c) and its putative protein (Tke) contains a N-terminal LysM peptidoglycan binding domain and a M23 putative catalytic site in the C-terminal part. No cognate immune protein was identified around the Tke potential effector, likely due to the lack of data in the immune protein database 36 . Bioinformatic analyses have shown that CH1157 Tke are mainly found in K. pneumoniae species and share specific domains of other T6SSs effectors (Type VI Amidase Effector (Tae) and Type VI Metallopeptidase Effector (Tpe)) 47 .…”

“…In vitro intra- and inter-species antibacterial activities have been associated with T6SS expression, and a phospholipase (Tle1 KP ) was identified as the effector of the multidrug resistant strain HS11286 and a toxin-antitoxin system including a phospholipase effector (Tle1 KP ) and its cognate immunity protein (Tli1 KP ) was identified in the multidrug resistant strain HS11286, conferring Tle1 KP resistance 30 . Other phospholipase T6SS effectors have already been identified in K. pneumoniae species (Tle3) 34 , but due to the diversity of T6SS effectors 35 , 36 others remain to be identified.…”