SO can I download and upgrade lion directly from Mac App Store?
sorry, no. installing 10.7 Lion or 10.8 Mountain Lion is a multi-step process. You must first be running 10.6.8 to have access to the Mac App Store (used in the second part). Either of these upgrades can be installed from 10.6.8, you do not have to use 10.7 to get to 10.8:
First you buy a download code for the version you want for US$20 from the Apple Online Store. It will be delivered to you in an email, and requires human intervention, so it takes a few days and will not happen over a weekend. Included in the email will be instructions about how to apply that code to your Apple-ID account at the Mac App Store.
Once the code is applied, you will get the appropriate version of the software added to your "Purchases" page at the Mac App Store, and will be able to download and re-download the actual software from there.
If you do not have 10.6.8 on an older Mac (typically around 2011 but there are many exceptions), you do not yet have a working version of the Mac App Store. To get 10.6.8 for those Macs, you buy and install the 10.6 Snow Leopard DVD, which contains 10.6.3. There are a few Macs from early 2011 that shipped with 10.6.6, and cannot run the "Full retail" DVD that contains 10.6.3, and those are a special case.