Naofumi Ito

Lactic Acid Bacteria Convert Human Fibroblasts to Multipotent Cells

The human gastrointestinal tract is colonized by a vast community of symbionts and commensals. Lactic acid bacteria (LAB) form a group of related, low-GC-content, gram-positive bacteria that are considered to offer a number of probiotic benefits to general health. While the role of LAB in gastrointestinal microecology has been the subject of extensive study, little is known about how commensal prokaryotic organisms directly influence eukaryotic cells. Here, we demonstrate the generation of multipotential cells from adult human dermal fibroblast cells by incorporating LAB. LAB-incorporated cell clusters are similar to embryoid bodies derived from embryonic stem cells and can differentiate into endodermal, mesodermal, and ectodermal cells in vivo and in vitro. LAB-incorporated cell clusters express a set of genes associated with multipotency, and microarray analysis indicates a remarkable increase of NANOG, a multipotency marker, and a notable decrease in HOX gene expression in LAB-incorporated cells. During the cell culture, the LAB-incorporated cell clusters stop cell division and start to express early senescence markers without cell death. Thus, LAB-incorporated cell clusters have potentially wide-ranging implications for cell generation, reprogramming, and cell-based therapy.

Reprogramming of human somatic cells by bacteria

In general, it had been believed that the cell fate restriction of terminally differentiated somatic cells was irreversible. In 1952, somatic cell nuclear transfer (SCNT) was introduced to study early embryonic development in frogs. So far, various mammalian species have been successfully cloned using the SCNT technique, though its efficiency is very low. Embryonic stem (ES) cells were the first pluripotent cells to be isolated from an embryo and have a powerful potential to differentiate into more than 260 types of cells. The generation of induced pluripotent stem (iPS) cells was a breakthrough in stem cell research, and the use of these iPS cells has solved problems such as low efficiency and cell fate restriction. These cells have since been used for clinical application, disease investigation, and drug selection. As it is widely accepted that the endosymbiosis of Archaea into eukaryotic ancestors resulted in the generation of eukaryotic cells, we examined whether bacterial infection could alter host cell fate. We previously showed that when human dermal fibroblast (HDF) cells were incorporated with lactic acid bacteria (LAB), the LAB‐incorporated HDF cells formed clusters and expressed a subset of common pluripotent markers. Moreover, LAB‐incorporated cell clusters could differentiate into cells derived from each of the three germinal layers both in vivo and in vitro, indicating successful reprogramming of host HDF cells by LAB. In the current review, we introduce the existing examples of cellular reprogramming by bacteria and discuss their nuclear reprogramming mechanisms.

Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency

Recently, we reported that bacterial incorporation induces cellular transdifferentiation of human fibroblasts. However, the bacterium-intrinsic cellular- transdifferentiation factor remained unknown. Here, we found that cellular transdifferentiation is caused by ribosomes. Ribosomes, isolated from both prokaryotic and eukaryotic cells, induce the formation of embryoid body-like cell clusters. Numerous ribosomes are incorporated into both the cytoplasm and nucleus through trypsin-activated endocytosis, which leads to cell-cluster formation. Although ribosome-induced cell clusters (RICs) express several stemness markers and differentiate into derivatives of all three germ layers in heterogeneous cell populations, RICs fail to proliferate, alter the methylation states of pluripotent genes, or contribute to teratoma or chimera formation. However, RICs express markers of epithelial–mesenchymal transition without altering the cell cycle, despite their proliferation obstruction. These findings demonstrate that incorporation of ribosomes into host cells induces cell transdifferentiation and alters cellular plasticity.

Involvement of Tsukushi in diverse developmental processes

Tsukushi (TSK) is a small signaling molecule which takes part in different developmental processes of multiple vertebrate organisms. The diverse activity of TSK depends on its ability to bind various intermediate molecules from different major signaling pathways. Interactions of TSK with BMP, FGF, TGF-β and Wnt pathways have already been confirmed. In this review, we will introduce the latest information regarding the involvement of TSK in developmental events. We suggest a fine tuning role for TSK in multiple signaling cascades. Also, we recommend further studies on the developmental role of TSK to fully reveal its potential.

An extracellular [NiFe] hydrogenase mediating iron corrosion is encoded in a genetically unstable genomic island in Methanococcus maripaludis

Certain methanogens deteriorate steel surfaces through a process called microbiologically influenced corrosion (MIC). However, the mechanisms of MIC, whereby methanogens oxidize zerovalent iron (Fe0), are largely unknown. In this study, Fe0-corroding Methanococcus maripaludis strain OS7 and its derivative (strain OS7mut1) defective in Fe0-corroding activity were isolated. Genomic analysis of these strains demonstrated that the strain OS7mut1 contained a 12-kb chromosomal deletion. The deleted region, termed “MIC island”, encoded the genes for the large and small subunits of a [NiFe] hydrogenase, the TatA/TatC genes necessary for the secretion of the [NiFe] hydrogenase, and a gene for the hydrogenase maturation protease. Thus, the [NiFe] hydrogenase may be secreted outside the cytoplasmic membrane, where the [NiFe] hydrogenase can make direct contact with Fe0, and oxidize it, generating hydrogen gas: Fe0 + 2 H+ → Fe2+ + H2. Comparative analysis of extracellular and intracellular proteomes of strain OS7 supported this hypothesis. The identification of the MIC genes enables the development of molecular tools to monitor epidemiology, and to perform surveillance and risk assessment of MIC-inducing M. maripaludis.

Reprogramming of Cells by Lactic Acid Bacteria

Living organisms have been classified into three domains—archaea, eukaryota, and prokaryota—based on their cell structure and genetic evolution (Woese CR, Kandler O, Wheelis ML. Proc Natl Acad Sci USA 87:4576–4579, 1990). The eukaryotic cells have organelles that originated from prokaryotes living within these cells as endosymbionts (Martin W, Hoffmeister M, Rotte C, Henze K. Biol Chem 382:1521–1539. https://doi.org/10.1515/BC.2001.187, 2001). Endosymbionts affected the evolution and diversity of living organisms by horizontal gene transfer (Woese CR. Proc Natl Acad Sci USA 99:8742–8747. https://doi.org/10.1073/pnas.132266999, 2002; Timmis JN, Ayliffe MA, Huang CY, Martin W. Nat Rev Genet 5:123–135. https://doi.org/10.1038/nrg1271, 2004). The origin of eukaryotic cells was explained by the endosymbiotic theory, which has been advanced and substantiated with microbiological evidence (Margulis L. Origin of eukaryotic cells: evidence and research implications for a theory of the origin and evolution of microbial, plant and animal cells on the precambrian earth. Yale University Press, New Heaven, 1970). The partnership between a primitive anaerobic eukaryotic predator cell and an aerobic bacterial cell was potentially established about 1.5 billion years ago. At present, it is widely believed that eubacteria infected archaebacteria, leading to the translocation of genomic DNA and the evolution of eukaryotic cells (Hartman H, Fedorov A. Proc Natl Acad Sci USA 99:1420–1425. https://doi.org/10.1073/pnas.032658599, 2002). Over time, endosymbiotic interactions and genomic scrambling in various organisms contributed to the generation of new organisms.

Transdifferentiation of human somatic cells by ribosome

Ribosomes are intracellular organelles ubiquitous in all organisms, which translate information from mRNAs to synthesize proteins. They are complex macromolecules composed of dozens of proteins and ribosomal RNAs. Other than translation, some ribosomal proteins also have side‐jobs called “Moonlighting” function. The majority of these moonlighting functions influence cancer progression, early development and differentiation. Recently, we discovered that ribosome is involved in the regulation of cellular transdifferentiation of human dermal fibroblasts (HDFs). In vitro incorporation of ribosomes into HDFs arrests cell proliferation and induces the formation of cell clusters, that differentiate into three germ layer derived cells upon induction by differentiation mediums. The discovery of ribosome induced transdifferentiation, that is not based on genetic modification, find new possibilities for the treatment of cancer and congenital diseases, as well as to understand early development and cellular lineage differentiation.