Clever DNA tricks – Ars Technica

Each person begins as a single fertilized egg. By adulthood, that single cell has turned into approximately 37 trillion cells, many of which continue dividing to produce the same amount of new human cells every few months.

But those cells face an enormous challenge. 3.2 divided cell average should be copied one billion base pairs of DNA, about once every 24 hours. The cell’s replication machinery does an amazing job, copying genetic material at a fragmented rate of about 50 base pairs per second.

However, this is very slow to replicate a human genes. If a cell’s copying machinery starts at the head of each of its 46 chromosomes at the same time, it will finish off the longest chromosome—no. 1, at 249 million base pairs – in about two months.

says James Berger, a structural biologist at Johns Hopkins University School of Medicine in Baltimore and co-author Essay on DNA replication in eukaryotes In Biochemistry Annual Review 2021. Yeast cells have hundreds of potential reproductive origins, as they are called, and animals like mice and humans have tens of thousands of them, spread throughout their genomes.

“But that presents its own challenge, which is, how do you know where to start, and how do you time everything?” Berger says. Without careful control, some DNA may be copied twice, causing cellular frenzy.

Maintaining a tight grip on the DNA replication process is particularly important to avoid this hoopla. Today, researchers are taking steps toward a more complete understanding of the molecular checks and balances that have evolved in order to ensure that each parent begins to copy DNA only once, to accurately produce a new, complete genome.

Do it right, do it fast

Bad things can happen if replication does not start properly. For DNA to be copied, the DNA double helix must open, and the resulting single strands—each serving as a template for building a new second strand—are susceptible to breaking. Or the process could crash. “You really want to solve redundancy quickly,” says John Devley, a biochemist at the Francis Crick Institute in London. Problems during DNA replication can cause the genome to become disorganized, which is often an essential step on the road to cancer.

Some genetic diseases are also caused Problems with DNA replication. For example, Meyer-Gorlin syndrome, which involves short stature, small ears, and small or no kneecaps, is caused by mutations in several genes that help start the process of DNA replication.

It takes a tightly coordinated dance of dozens of proteins for the DNA-replication machinery to begin replicating at the correct point in a cell’s life cycle. The researchers have a pretty good idea of ​​which proteins do what, because they were able to make DNA replication happen in cell-free biological mixtures in the lab. They mimic the first critical steps in initiating replication using proteins from yeast– the same kind used to make bread and beer – and they’ve imitated a lot of the whole replication process Using human copies of replication proteinsalso.

The cell controls the initiation of DNA replication in a two-step process. The whole point of this process is to control the actions of a crucial enzyme — called helicase — that unwinds the double helix of DNA in preparation for its transcription. In the first step, inactive helicases are loaded onto the DNA at the origin, where replication is initiated. During the second step, the helicase is activated, to decode the DNA.

Ready (download helicase)…

The process begins with a group of six proteins sitting at the origin. This group is called ORC In the form of a double layer ring Berger’s team found that it had a handy slot that allowed it to slide into strands of DNA.

In baker’s yeast, a favorite of scientists studying DNA replication, these start sites are easy to spot: They contain a specific basic DNA sequence of 11 to 17 letters long, rich in the chemical bases adenine and thymine. Scientists watched as an orc grabbed DNA and then slid along, Find the origin sequence Until he finds the right place.

But in humans and other complex life forms, the initiation sites are not clearly defined, and it’s not entirely clear what causes an orc to snap and hold, says Alessandro Costa, a structural biologist at the Crick Institute who, with Devley, wrote About the initiation of DNA replication In the 2022 Annual Review of Biochemistry. It seems likely that replication will begin in places where the genome—usually tightly wrapped around proteins called histones—has loosened up.

Once the ORC rests on the DNA, it attracts a second protein complex: one that includes the helix that will eventually unwind the DNA. Costa and colleagues used electron microscopy to see how orcs are used Lures at first one helicase, then another. The helicase is also ring-shaped, and each one unfolds to wrap around the double-stranded DNA. Then the two planes close again, facing each other on the strands of DNA, like two beads on a string.

At first, they just sit there, like cars with no gas in the tank. It has not yet been activated, and at the moment, the cell goes about its usual work.

Get a set (Helicase Activation)…

Things get started really quickly when an important molecule called CDK waves the green flag, triggering a jump in chemical steps that lure in more proteins. One of them is DNA polymerase—what Costa calls the “typewriter” that will build new DNA strands—which attaches to each helicase. Others activate helicases, which can now burn energy to flow along the DNA.

When this happens, it changes the shape of the helicases, pushing one strand of DNA and pulling the other. This creates stress on the weak hydrogen bonds that normally hold the two strands together by the bases – the As, Cs, Ts and Gs that make up the rungs of the DNA ladder. The tufts are torn. Costa and his colleagues have observed how these two helicopters were decipher the DNA between themAnd they’ve seen how planes keep untethered bases stable and out of the way.

He goes!

In the beginning, both states were wrapped around both strands of DNA, and they couldn’t reach far like this, because they were facing each other and would bump into each other. But then they both undergo a reposition, spitting one strand of DNA or the other out of the loop. Now separated, they can crowd on each other, and replication continues apace.

Each helicase motor moves along its own individual thread, in the opposite direction to the other. They leave the origin behind and move away from the hydrogen-bonded base pairs as they travel. DNA polymerase is right behind it, transcribing DNA letters when they are freed from their partners.

The CDK’s second task is to prevent any other aircraft from hopping onto the assets. Thus, there is a single start of replication for each parentage, which ensures proper transcription of the genome – even though transcription does not start at the same time at every site. The entire process of DNA replication in human cells takes about eight hours.

There is still a lot to do. For one thing, the DNA being copied is not a naked double helix. It’s wrapped around histones and attached to a lot of other proteins that get involved in turning genes on or off Making copies of genes from RNA. How do these flux proteins influence each other and avoid conflict with each other?

In addition to this fascinating basic biology–a fascinating process that is necessary for all life on Earth–there are implications for diseases such as cancer. Scientists already know that faulty replication can destabilize DNA, and an unstable genome prone to mutation may be an early hallmark of cancer development. delusion Further investigation Links between replication proteins and cancer.

“I think there are opportunities for therapeutic interventions for these systems,” says Berger, “once we have enough insights into how they work and what they look like.”

amber dance, a science writer in the Los Angeles area, also likes to break big tasks down into smaller pieces: She took me five days to complete the drafting steps for this article. This article originally appeared in Well-known magazine, an independent journalistic endeavor from Annual Reviews. Sign up the news.